In no particular order since this list shifts a bit except the top two.

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The Legend of Zelda: A Link to the Past

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Mega Man II

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Final Fantasy VI

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Metal Gear Solid 3: Snake Eater

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Chrono Trigger

Honorable Mentions: Shin Megami Tensei III: Nocturne, Persona 3: FES, Mega Man X, Xenogears, Final Fantasy Tactics, Suikoden II, Castlevania: Symphony of the Night, and Street Fighter II.